diff 07_per_base_n_content.Rmd @ 11:507eec497730 draft

update fastqc site

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/07_per_base_n_content.Rmd	Tue Nov 07 16:52:24 2017 -0500
@@ -0,0 +1,43 @@
+---
+title: 'Per base N content'
+output:
+    html_document:
+      number_sections: true
+      toc: true
+      theme: cosmo
+      highlight: tango
+---
+
+```{r setup, include=FALSE, warning=FALSE, message=FALSE}
+knitr::opts_chunk$set(
+  echo = ECHO,
+  error = TRUE
+)
+```
+
+### Per base N content
+
+```{r 'Per base N content', fig.width=10}
+## reads 1
+pbNc_1 = extract_data_module('REPORT_DIR/reads_1_fastqc_data.txt', 'Per base N content')
+pbNc_1$id = 1:length(pbNc_1$X.Base)
+pbNc_1$trim = 'before'
+
+## reads 2
+pbNc_2 = extract_data_module('REPORT_DIR/reads_2_fastqc_data.txt', 'Per base N content')
+pbNc_2$id = 1:length(pbNc_2$X.Base)
+pbNc_2$trim = 'after'
+
+comb_pbNc = rbind(pbNc_1, pbNc_2)
+comb_pbNc$trim = factor(levels = c('before', 'after'), comb_pbNc$trim)
+
+p = ggplot(data = comb_pbNc, aes(x = id, y = N.Count)) +
+  geom_line(color = 'red') +
+  scale_x_continuous(breaks = pbNc_2$id, labels = pbNc_2$X.Base) + 
+  facet_grid(. ~ trim) +
+  ylim(0, 1) + 
+  xlab('N-Count') +
+  ylab('') + 
+  theme(axis.text.x = element_text(angle=45))
+ggplotly(p)
+```
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